lamindb_setup 0.81.4__py3-none-any.whl → 1.0a5__py3-none-any.whl

lamindb_setup/core/upath.py

@@ -12,14 +12,15 @@ from itertools import islice
 from pathlib import Path, PosixPath, PurePosixPath, WindowsPath
 from typing import TYPE_CHECKING, Any, Literal
 
+import click
 import fsspec
 from lamin_utils import logger
 from upath import UPath
-from upath.implementations.cloud import CloudPath, S3Path  # keep CloudPath!
+from upath.implementations.cloud import CloudPath  # keep CloudPath!
 from upath.implementations.local import LocalPath
 
 from ._aws_credentials import HOSTED_BUCKETS, get_aws_credentials_manager
-from .hashing import HASH_LENGTH, b16_to_b64, hash_from_hashes_list
+from .hashing import HASH_LENGTH, b16_to_b64, hash_from_hashes_list, hash_string
 
 if TYPE_CHECKING:
     from .types import UPathStr
@@ -192,12 +193,15 @@ class ProgressCallback(fsspec.callbacks.Callback):
     def update_relative_value(self, inc=1):
         if inc != 0:
             self.value += inc
-        # this is specific to http filesystem
-        # for some reason the last update is 0 always
-        # here 100% is forced manually in this case
-        elif self.value >= 0.999:
-            self.value = self.size
-        self.call()
+            self.call()
+        else:
+            # this is specific to http filesystem
+            # for some reason the last update is 0 always
+            # sometimes the reported result is less that 100%
+            # here 100% is forced manually in this case
+            if self.value < 1.0 and self.value >= 0.999:
+                self.value = self.size
+                self.call()
 
     def branch(self, path_1, path_2, kwargs):
         if self.adjust_size:
@@ -264,7 +268,17 @@ def download_to(self, local_path: UPathStr, print_progress: bool = True, **kwarg
         )
         kwargs["callback"] = callback
 
-    self.fs.download(str(self), str(local_path), **kwargs)
+    cloud_path_str = str(self)
+    local_path_str = str(local_path)
+    # needed due to https://github.com/fsspec/filesystem_spec/issues/1766
+    # otherwise fsspec calls fs._ls_real where it reads the body and parses links
+    # so the file is downloaded 2 times
+    # upath doesn't call fs.ls to infer type, so it is safe to call
+    if self.protocol in {"http", "https"} and self.stat().as_info()["type"] == "file":
+        self.fs.use_listings_cache = True
+        self.fs.dircache[cloud_path_str] = []
+
+    self.fs.download(cloud_path_str, local_path_str, **kwargs)
 
 
 def upload_from(
@@ -312,8 +326,7 @@ def upload_from(
         destination = self.as_posix()
 
     # the below lines are to avoid s3fs triggering create_bucket in upload if
-    # dirs are present it allows to avoid permission error
-    # would be easier to just
+    # dirs are present, it allows to avoid the permission error
     if self.protocol == "s3" and local_path_is_dir and create_folder:
         bucket = self.drive
         if bucket not in self.fs.dircache:
@@ -505,7 +518,7 @@ def compute_file_tree(
         skip_suffixes_tuple = ()
     else:
         skip_suffixes_tuple = tuple(skip_suffixes)  # type: ignore
-    n_objects = 0
+    n_files = 0
     n_directories = 0
 
     # by default only including registered files
@@ -518,7 +531,7 @@ def compute_file_tree(
         include_paths = set()
 
     def inner(dir_path: Path, prefix: str = "", level: int = -1):
-        nonlocal n_objects, n_directories, suffixes
+        nonlocal n_files, n_directories, suffixes
         if level == 0:
             return
         stripped_dir_path = dir_path.as_posix().rstrip("/")
@@ -551,7 +564,7 @@ def compute_file_tree(
                 suffix = extract_suffix_from_path(child_path)
                 suffixes.add(suffix)
                 n_files_per_dir_and_type[suffix] += 1
-                n_objects += 1
+                n_files += 1
                 if n_files_per_dir_and_type[suffix] == n_max_files_per_dir_and_type:
                     yield prefix + "..."
                 elif n_files_per_dir_and_type[suffix] > n_max_files_per_dir_and_type:
@@ -564,15 +577,15 @@ def compute_file_tree(
     for line in islice(iterator, n_max_files):
         folder_tree += f"\n{line}"
     if next(iterator, None):
-        folder_tree += f"\n... only showing {n_max_files} out of {n_objects} files"
+        folder_tree += f"\n... only showing {n_max_files} out of {n_files} files"
     directory_info = "directory" if n_directories == 1 else "directories"
     display_suffixes = ", ".join([f"{suffix!r}" for suffix in suffixes])
-    suffix_message = f" with suffixes {display_suffixes}" if n_objects > 0 else ""
+    suffix_message = f" with suffixes {display_suffixes}" if n_files > 0 else ""
     message = (
         f"{n_directories} sub-{directory_info} &"
-        f" {n_objects} files{suffix_message}\n{path.resolve()}{folder_tree}"
+        f" {n_files} files{suffix_message}\n{path.resolve()}{folder_tree}"
     )
-    return message, n_objects
+    return message, n_files
 
 
 # adapted from: https://stackoverflow.com/questions/9727673
@@ -726,12 +739,26 @@ warnings.filterwarnings(
 )
 
 
-def create_path(path: UPath, access_token: str | None = None) -> UPath:
-    path = UPath(path)
-    # test whether we have an AWS S3 path
-    if not isinstance(path, S3Path):
-        return path
-    return get_aws_credentials_manager().enrich_path(path, access_token)
+def create_path(path: UPathStr, access_token: str | None = None) -> UPath:
+    upath = UPath(path)
+
+    if upath.protocol == "s3":
+        # add managed credentials and other options for AWS s3 paths
+        return get_aws_credentials_manager().enrich_path(upath, access_token)
+
+    if upath.protocol in {"http", "https"}:
+        # this is needed because by default aiohttp drops a connection after 5 min
+        # so it is impossible to download large files
+        client_kwargs = upath.storage_options.get("client_kwargs", {})
+        if "timeout" not in client_kwargs:
+            from aiohttp import ClientTimeout
+
+            client_kwargs = {
+                **client_kwargs,
+                "timeout": ClientTimeout(sock_connect=30, sock_read=30),
+            }
+            return UPath(upath, client_kwargs=client_kwargs)
+    return upath
 
 
 def get_stat_file_cloud(stat: dict) -> tuple[int, str | None, str | None]:
@@ -749,20 +776,26 @@ def get_stat_file_cloud(stat: dict) -> tuple[int, str | None, str | None]:
     # s3
     # StorageClass is checked to be sure that it is indeed s3
     # because http also has ETag
-    elif "ETag" in stat and "StorageClass" in stat:
+    elif "ETag" in stat:
         etag = stat["ETag"]
-        # small files
-        if "-" not in etag:
-            # only store hash for non-multipart uploads
-            # we can't rapidly validate multi-part uploaded files client-side
-            # we can add more logic later down-the-road
-            hash = b16_to_b64(etag)
-            hash_type = "md5"
+        if "mimetype" in stat:
+            # http
+            hash = hash_string(etag.strip('"'))
+            hash_type = "md5-etag"
         else:
-            stripped_etag, suffix = etag.split("-")
-            suffix = suffix.strip('"')
-            hash = b16_to_b64(stripped_etag)
-            hash_type = f"md5-{suffix}"  # this is the S3 chunk-hashing strategy
+            # s3
+            # small files
+            if "-" not in etag:
+                # only store hash for non-multipart uploads
+                # we can't rapidly validate multi-part uploaded files client-side
+                # we can add more logic later down-the-road
+                hash = b16_to_b64(etag)
+                hash_type = "md5"
+            else:
+                stripped_etag, suffix = etag.split("-")
+                suffix = suffix.strip('"')
+                hash = b16_to_b64(stripped_etag)
+                hash_type = f"md5-{suffix}"  # this is the S3 chunk-hashing strategy
     if hash is not None:
         hash = hash[:HASH_LENGTH]
     return size, hash, hash_type
@@ -787,17 +820,18 @@ def get_stat_dir_cloud(path: UPath) -> tuple[int, str | None, str | None, int]:
         if compute_list_hash:
             hashes.append(object[accessor].strip('"='))
     size = sum(sizes)
-    n_objects = len(sizes)
+    n_files = len(sizes)
     if compute_list_hash:
         hash, hash_type = hash_from_hashes_list(hashes), "md5-d"
-    return size, hash, hash_type, n_objects
+    return size, hash, hash_type, n_files
 
 
-class InstanceNotEmpty(Exception):
-    pass
+class InstanceNotEmpty(click.ClickException):
+    def show(self, file=None):
+        pass
 
 
-# is as fast as boto3: https://lamin.ai/laminlabs/lamindata/transform/krGp3hT1f78N5zKv
+# is as fast as boto3: https://lamin.ai/laminlabs/lamin-site-assets/transform/krGp3hT1f78N5zKv
 def check_storage_is_empty(
     root: UPathStr, *, raise_error: bool = True, account_for_sqlite_file: bool = False
 ) -> int:
@@ -820,20 +854,20 @@ def check_storage_is_empty(
             root_string += "/"
         directory_string = root_string + ".lamindb"
     objects = root_upath.fs.find(directory_string)
-    n_objects = len(objects)
-    n_diff = n_objects - n_offset_objects
+    n_files = len(objects)
+    n_diff = n_files - n_offset_objects
     ask_for_deletion = (
         "delete them prior to deleting the instance"
         if raise_error
         else "consider deleting them"
     )
     message = (
-        f"Storage '{directory_string}' contains {n_objects - n_offset_objects} objects"
+        f"Storage '{directory_string}' contains {n_files - n_offset_objects} objects"
         f" - {ask_for_deletion}"
     )
     if n_diff > 0:
         if raise_error:
-            raise InstanceNotEmpty(message)
+            raise InstanceNotEmpty(message) from None
         else:
             logger.warning(message)
     return n_diff

{lamindb_setup-0.81.4.dist-info → lamindb_setup-1.0a5.dist-info}/METADATA

@@ -1,20 +1,19 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: lamindb_setup
-Version: 0.81.4
+Version: 1.0a5
 Summary: Setup & configure LaminDB.
 Author-email: Lamin Labs <open-source@lamin.ai>
 Requires-Python: >=3.9
 Description-Content-Type: text/markdown
-Requires-Dist: lnschema_core>=0.51.0
 Requires-Dist: lamin_utils>=0.3.3
-Requires-Dist: django>4.2,<5.3.0
+Requires-Dist: django>=5,<5.2
 Requires-Dist: dj_database_url>=1.3.0,<3.0.0
 Requires-Dist: pydantic-settings
 Requires-Dist: appdirs<2.0.0
 Requires-Dist: requests
 Requires-Dist: universal_pathlib==0.2.5
 Requires-Dist: botocore<2.0.0
-Requires-Dist: supabase>=2.8.1,<=2.10.0
+Requires-Dist: supabase>=2.8.1,<=2.11.0
 Requires-Dist: psutil
 Requires-Dist: urllib3<2 ; extra == "aws"
 Requires-Dist: aiobotocore[boto3]>=2.5.4,<3.0.0 ; extra == "aws"

lamindb_setup-1.0a5.dist-info/RECORD

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{lamindb_setup-0.81.4.dist-info → lamindb_setup-1.0a5.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: flit 3.9.0
+Generator: flit 3.10.1
 Root-Is-Purelib: true
 Tag: py3-none-any

lamindb_setup-0.81.4.dist-info/RECORD

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